PROJECT SUMMARY The vast majority of individual susceptibility to sickness and disease in humans is generated by complex interactions between multiple genetic loci and the environment, yet we still have very little understanding of how the map between genotype and phenotype is structured or how this structure influences the response to the environment and long-term evolutionary change. In particular, complex genetic networks should generate pleiotropic relationships among traits whose functional coupling can make individual effects difficult to examine using traditional knockout approaches. Although the structure of these networks is known to be strongly influenced by genomic context, both in terms of their immediate functional response and in the long-term evolution of their structure, we still have little understanding of how all of these factors interact within complex living systems. The goal of this project is to address these questions as part of a broad research framework using three specific experimental paradigms with the nematode Caenorhabditis elegans and its relatives as model systems: (1) How are complex regulatory systems structured and how does this structure determine their evolutionary dynamics?, (2) What are the drivers of genomic hyperdiversity and how can this diversity be used as a tool to understand the evolution of genetic systems?, and (3) How does the genomic landscape of variation, recombination and sexual reproduction influence the response to selection? These questions will be addressed using an innovative integration of approaches drawn from genomics, single-cell analysis, microfluidic engineering, high-throughput phenotyping, genetic transformation, and computational biology. This research uses a systems-genetics approach that integrates an understanding of natural genetic variation within a strong functional hypothesis-testing framework to understand the function and evolution of complex regulatory systems with critical implications for human health.